This all adds up to ¥ 40,460, ideally you'd use a 7 Day JR Pass to cover your your most expansive legs (Hakone - Kyoto - Nagano - Tokyo) however since these travel days most that 7 days apart it would not really work. So you could either buy normal tickets as you travel or try to rearrange a little to cover the more expansive routes with a JR Pass.

Alternatively you could consider a 14 Day JR Pass (¥ 45,100) and cover the all of your journey. With a little more travel it would quickly become worth it. For instance a day trip to Nikko or Hiroshima would already make the JR Pass pay of and help you make the most of your JR Pass.